GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Phyllobacterium endophyticum PEPV15

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_106719055.1 CU100_RS23405 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_003010935.1:WP_106719055.1
          Length = 395

 Score =  524 bits (1349), Expect = e-153
 Identities = 247/367 (67%), Positives = 302/367 (82%), Gaps = 2/367 (0%)

Query: 17  FPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGW 76
           F A++PL LDSG  +    IAYQ YG+LNADKSNA+L+CHALTGDQHVA+ HP TGKPGW
Sbjct: 28  FGADKPLHLDSGVSLSPFRIAYQAYGELNADKSNAILVCHALTGDQHVANVHPVTGKPGW 87

Query: 77  WQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQ 136
           W+ L+GPGKP+D  R+F+ICSNV+GGC+GSTGPASINP TGK Y L  P+ITIADMVRAQ
Sbjct: 88  WELLIGPGKPIDTDRYFVICSNVLGGCLGSTGPASINPETGKPYALDLPIITIADMVRAQ 147

Query: 137 AMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGR 196
           AMLV   G+E LFAV+GGSMGGMQV +WA  + +++F+AV +A+ +RHS+QNIAFHEVGR
Sbjct: 148 AMLVEHFGIEQLFAVIGGSMGGMQVLEWASSHSDKVFAAVAIATGARHSSQNIAFHEVGR 207

Query: 197 QAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGF 255
           QA+MADP+W+ G Y E G  P KGL+VARMAAHITYLSE AL  KFGR LQ R  +++GF
Sbjct: 208 QAVMADPEWKEGRYLEAGTVPRKGLSVARMAAHITYLSETALHNKFGRNLQDRQNVTFGF 267

Query: 256 DADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCV 315
           DADFQ+ESYLRHQG++FV+RFD NSYLY+TRAMDYFD+AA HGG LA AF  ++  RFC+
Sbjct: 268 DADFQIESYLRHQGTTFVERFDPNSYLYMTRAMDYFDLAAEHGGRLADAFAGSK-TRFCI 326

Query: 316 LSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLASA 375
           +SF+SDWL+PT+E+R +  AL AAGA  +F EIESD+GHD+FLLDEP M + + GF+ SA
Sbjct: 327 VSFTSDWLFPTSESRMVAHALNAAGASVSFVEIESDRGHDSFLLDEPEMFSTITGFIRSA 386

Query: 376 ERDRGLV 382
            R RGLV
Sbjct: 387 ARARGLV 393


Lambda     K      H
   0.321    0.135    0.417 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 521
Number of extensions: 18
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 382
Length of database: 395
Length adjustment: 30
Effective length of query: 352
Effective length of database: 365
Effective search space:   128480
Effective search space used:   128480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_106719055.1 CU100_RS23405 (homoserine O-acetyltransferase)
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01392.hmm
# target sequence database:        /tmp/gapView.1200511.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01392  [M=351]
Accession:   TIGR01392
Description: homoserO_Ac_trn: homoserine O-acetyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-148  479.6   0.0   3.2e-148  479.4   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106719055.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106719055.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.4   0.0  3.2e-148  3.2e-148       2     350 ..      31     383 ..      30     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.4 bits;  conditional E-value: 3.2e-148
                             TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsry 73 
                                           +++l+l+sG  ls +++ay+ yG+lna+++Na+lvcHaltg++hva+ +  + k GWW+ l+Gpg+++dt+ry
  NCBI__GCF_003010935.1:WP_106719055.1  31 DKPLHLDSGVSLSPFRIAYQAYGELNADKSNAILVCHALTGDQHVANVHPVTGKpGWWELLIGPGKPIDTDRY 103
                                           589********************************************99977767****************** PP

                             TIGR01392  74 fvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewa 146
                                           fv+c+NvlG+c GstgP+sinpetgkpy  ++P +ti D+v+aq++l++++g+e+l+av+GgS+GGmq+lewa
  NCBI__GCF_003010935.1:WP_106719055.1 104 FVICSNVLGGCLGSTGPASINPETGKPYALDLPIITIADMVRAQAMLVEHFGIEQLFAVIGGSMGGMQVLEWA 176
                                           ************************************************************************* PP

                             TIGR01392 147 lsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesl 218
                                            s  ++v ++v++at+ar+s+q+iaf+ev rqa+++Dpe+++G+y e +  P+kGL++ARm a++tY+se++l
  NCBI__GCF_003010935.1:WP_106719055.1 177 SSHSDKVFAAVAIATGARHSSQNIAFHEVGRQAVMADPEWKEGRYLEAGtVPRKGLSVARMAAHITYLSETAL 249
                                           ***********************************************999*********************** PP

                             TIGR01392 219 eerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkika 291
                                           +++fgr+ ++++++++ ++++f++esylr+qg++fverFd nsYl++t+a+d++dla+++ ++l++a++  k+
  NCBI__GCF_003010935.1:WP_106719055.1 250 HNKFGRNLQDRQNVTFGFDADFQIESYLRHQGTTFVERFDPNSYLYMTRAMDYFDLAAEHGGRLADAFAGSKT 322
                                           ************************************************************************* PP

                             TIGR01392 292 pvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                           ++++v+++sD+lf+++e++ +a+al+aa+++  ++eies++GHD+Fll++ ++ ++i+ f+
  NCBI__GCF_003010935.1:WP_106719055.1 323 RFCIVSFTSDWLFPTSESRMVAHALNAAGASvsFVEIESDRGHDSFLLDEPEMFSTITGFI 383
                                           ****************************99999**********************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (395 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.71
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory